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(-) Description

Title :  HUMAN VIMENTIN COIL 1A FRAGMENT (1A)
 
Authors :  S. V. Strelkov, H. Herrmann, N. Geisler, R. Zimbelmann, U. Aebi, P. Burkhard
Date :  08 Aug 01  (Deposition) - 15 Mar 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Vimentin, Intermediate Filament, Heptad Repeat (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Strelkov, H. Herrmann, N. Geisler, T. Wedig, R. Zimbelmann, U. Aebi, P. Burkhard
Conserved Segments 1A And 2B Of The Intermediate Filament Dimer: Their Atomic Structures And Role In Filament Assembly.
Embo J. V. 21 1255 2002
PubMed-ID: 11889032  |  Reference-DOI: 10.1093/EMBOJ/21.6.1255
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - VIMENTIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Fragment1A, RESIDUES 102-138
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsTWO EXTRA RESIDUES, GS, AT THE N-TERMINUS ARE RESULT OF THE CLONING PROCEDURE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:100 , SER A:101 , ASN A:102 , GLU A:103 , VAL A:105 , GLU A:106BINDING SITE FOR RESIDUE SO4 A1139

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1GK7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1GK7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1GK7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1GK7)

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.3dENST000002242373dENSE00002186269chr10:17271277-17271984708VIME_HUMAN1-1881881A:100-13839
1.4cENST000002242374cENSE00001270958chr10:17272649-1727270961VIME_HUMAN188-208210--
1.5bENST000002242375bENSE00000692805chr10:17275586-1727568196VIME_HUMAN209-240320--
1.6ENST000002242376ENSE00000692809chr10:17275769-17275930162VIME_HUMAN241-294540--
1.7aENST000002242377aENSE00000692812chr10:17276692-17276817126VIME_HUMAN295-336420--
1.8aENST000002242378aENSE00001270949chr10:17277168-17277388221VIME_HUMAN337-410740--
1.8cENST000002242378cENSE00001121153chr10:17277845-1727788844VIME_HUMAN410-425160--
1.8eENST000002242378eENSE00000815998chr10:17278293-1727837886VIME_HUMAN425-453290--
1.9ENST000002242379ENSE00001906870chr10:17279229-17279592364VIME_HUMAN454-466130--

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:39
 aligned with VIME_HUMAN | P08670 from UniProtKB/Swiss-Prot  Length:466

    Alignment length:39
                                   109       119       129         
           VIME_HUMAN   100 RTNEKVELQELNDRFANYIDKVRFLEQQNKILLAELEQL 138
               SCOP domains d1gk7a_ A: Vimentin coil                SCOP domains
               CATH domains --------------------------------------- CATH domains
               Pfam domains --------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------- PROSITE
               Transcript 1 Exon 1.3d  PDB: A:100-138 [INCOMPLETE]  Transcript 1
                 1gk7 A 100 GSNEKVELQELNDRFANYIDKVRFLEQQNKILLAELEQL 138
                                   109       119       129         

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1GK7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1GK7)

(-) Gene Ontology  (32, 32)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (VIME_HUMAN | P08670)
molecular function
    GO:0003725    double-stranded RNA binding    Interacting selectively and non-covalently with double-stranded RNA.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:1990254    keratin filament binding    Interacting selectively and non-covalently with a keratin filament, an intermediate filament composed of acidic and basic keratins (types I and II), typically expressed in epithelial cells.
    GO:0008022    protein C-terminus binding    Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0097110    scaffold protein binding    Interacting selectively and non-covalently with a scaffold protein. Scaffold proteins are crucial regulators of many key signaling pathways. Although not strictly defined in function, they are known to interact and/or bind with multiple members of a signaling pathway, tethering them into complexes.
    GO:0005200    structural constituent of cytoskeleton    The action of a molecule that contributes to the structural integrity of a cytoskeletal structure.
    GO:0005212    structural constituent of eye lens    The action of a molecule that contributes to the structural integrity of the lens of an eye.
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
    GO:0060020    Bergmann glial cell differentiation    The process in which neuroepithelial cells of the neural tube give rise to Brgmann glial cells, specialized bipotential progenitors cells of the cerebellum. Differentiation includes the processes involved in commitment of a cell to a specific fate.
    GO:0060395    SMAD protein signal transduction    The cascade of processes by which a signal interacts with a receptor, causing a change in the activity of a SMAD protein, and ultimately effecting a change in the functioning of the cell.
    GO:0014002    astrocyte development    The process aimed at the progression of an astrocyte over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. An astrocyte is the most abundant type of glial cell. Astrocytes provide support for neurons and regulate the environment in which they function.
    GO:0045109    intermediate filament organization    Control of the spatial distribution of intermediate filaments; includes organizing filaments into meshworks, bundles, or other structures, as by cross-linking.
    GO:0045103    intermediate filament-based process    Any cellular process that depends upon or alters the intermediate filament cytoskeleton, that part of the cytoskeleton comprising intermediate filaments and their associated proteins.
    GO:0070307    lens fiber cell development    The process whose specific outcome is the progression of a lens fiber cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a lens fiber cell fate. A lens fiber cell is any of the elongated, tightly packed cells that make up the bulk of the mature lens in a camera-type eye.
    GO:0006928    movement of cell or subcellular component    The directed, self-propelled movement of a cell or subcellular component without the involvement of an external agent such as a transporter or a pore.
    GO:0030049    muscle filament sliding    The sliding of actin thin filaments and myosin thick filaments past each other in muscle contraction. This involves a process of interaction of myosin located on a thick filament with actin located on a thin filament. During this process ATP is split and forces are generated.
    GO:0010977    negative regulation of neuron projection development    Any process that decreases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0031252    cell leading edge    The area of a motile cell closest to the direction of movement.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    GO:0005882    intermediate filament    A cytoskeletal structure that forms a distinct elongated structure, characteristically 10 nm in diameter, that occurs in the cytoplasm of eukaryotic cells. Intermediate filaments form a fibrous system, composed of chemically heterogeneous subunits and involved in mechanically integrating the various components of the cytoplasmic space. Intermediate filaments may be divided into five chemically distinct classes: Type I, acidic keratins; Type II, basic keratins; Type III, including desmin, vimentin and others; Type IV, neurofilaments and related filaments; and Type V, lamins.
    GO:0045111    intermediate filament cytoskeleton    Cytoskeletal structure made from intermediate filaments, typically organized in the cytosol as an extended system that stretches from the nuclear envelope to the plasma membrane. Some intermediate filaments run parallel to the cell surface, while others traverse the cytosol; together they form an internal framework that helps support the shape and resilience of the cell.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    GO:0005777    peroxisome    A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        VIME_HUMAN | P086701gk4 1gk6 3g1e 3klt 3s4r 3ssu 3swk 3trt 3uf1 4mcy 4mcz 4md0 4md5 4mdi 4mdj 4ypc 4yv3

(-) Related Entries Specified in the PDB File

1gk4 HUMAN VIMENTIN COIL 2B FRAGMENT (CYS2)
1gk6 HUMAN VIMENTIN COIL 2B FRAGMENT LINKED TO GCN4 LEUCINE ZIPPER (Z2B)